fix(extension): 产物收割排除代码副本+删 work 目录——输出契约校验语义不变

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

bioflow_kernel/cli/run_extension.py

@@ -266,27 +266,39 @@ def _find_code_dir(ext_dir: Path) -> Path | None:
     return None
 
 
-def _copy_code_tree(src: Path, dst: Path) -> None:
-    """把代码树复制进可写目录(shutil.copytree,目标已存在)。"""
+def _copy_code_tree(src: Path, dst: Path) -> set[str]:
+    """把代码树复制进可写目录;返回原始代码相对路径集合(收割时排除)。"""
     import shutil
+    rels: set[str] = set()
     if not src.is_dir():
-        return
-    for item in src.iterdir():
-        dest = dst / item.name
+        return rels
+    for item in src.rglob("*"):
+        rel = item.relative_to(src).as_posix()
+        dest = dst / rel
         if item.is_dir():
-            shutil.copytree(item, dest, dirs_exist_ok=True)
+            dest.mkdir(parents=True, exist_ok=True)
         else:
+            dest.parent.mkdir(parents=True, exist_ok=True)
             shutil.copy2(item, dest)
+            rels.add(rel)
+    return rels
 
 
-def _merge_tree(src: Path, dst: Path) -> None:
-    """把 src 全部内容合并进 dst(含子目录;同名覆盖)。"""
+def _harvest_outputs(src: Path, dst: Path, exclude: set[str]) -> None:
+    """把 src 内产物(排除原始代码路径)合并进 dst,保留相对路径。"""
     import shutil
-    for item in src.iterdir():
-        dest = dst / item.name
+    for item in src.rglob("*"):
+        rel = item.relative_to(src).as_posix()
+        if rel in exclude:
+            continue
+        # 排除路径是原始代码文件所在目录时也跳过其祖先目录本身
+        if any(rel == e or rel.startswith(e + "/") for e in exclude):
+            continue
+        dest = dst / rel
         if item.is_dir():
-            shutil.copytree(item, dest, dirs_exist_ok=True)
+            dest.mkdir(parents=True, exist_ok=True)
         else:
+            dest.parent.mkdir(parents=True, exist_ok=True)
             shutil.copy2(item, dest)
 
 
@@ -390,9 +402,9 @@ def main(argv: list[str] | None = None) -> int:
     # 2026-09-15 修复:代码挂载只读,但 18 用例语义是「cd 代码目录后脚本写
     # outputs/ 相对目录」。等价做法 = 把代码复制进可写 run_dir 执行,
     # 结束后把 run_dir 产物收割进 output_dir。显式 --work-dir 可覆盖。
-    work_dir = Path(args.work_dir) if args.work_dir else (output_dir / "work")
+    work_dir = Path(args.work_dir) if args.work_dir else (output_dir / "_work")
     work_dir.mkdir(parents=True, exist_ok=True)
-    _copy_code_tree(code_dir, work_dir)
+    code_rel_paths = _copy_code_tree(code_dir, work_dir)
     # 模板中 {code_dir} 指向可写副本(而非只读挂载)
     effective_code_dir = work_dir
 
@@ -439,9 +451,11 @@ def main(argv: list[str] | None = None) -> int:
     if code != EXIT_OK:
         print(f"[run_extension] command exited with code {code}", file=sys.stderr)
         return code
-    # 收割:work_dir 内全部产物(含 outputs/ 子目录与中间文件)合并进 output_dir
+    # 收割:work_dir 产物(排除原始代码文件)合并进 output_dir,然后删除 work 目录
     try:
-        _merge_tree(work_dir, output_dir)
+        _harvest_outputs(work_dir, output_dir, code_rel_paths)
+        import shutil
+        shutil.rmtree(work_dir, ignore_errors=True)
     except OSError as exc:
         print(f"[run_extension] 产物收割失败: {exc}", file=sys.stderr)
         return EXIT_SETUP